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Bioinformatics Vol. 16 no. 8 2000
Pages 678-684
© 2000 Oxford University Press

Original Paper

ComboScreen facilitates the multiplex hybridization-based screening of high-density clone arrays

D. Curtis Jamison 1, James W. Thomas 1 and Eric D. Green 1,

1 Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA

Received on December 15, 1999 ; revised on March 6, 2000 ; accepted on March 8, 2000

Motivation: The construction of physical maps based on bacterial clones [e.g. bacterial artificial chromosomes (BACs)] is valuable for a number of molecular genetics applications, including the high-resolution mapping of genomic regions of interest and the identification of clones suitable for systematic sequencing. A common approach for large-scale screening of bacterial clone libraries involves the hybridization of high-density arrays of immobilized, lysed colonies with collections of DNA probes. The use of a multiplex hybridization screening strategy, whereby pooled probes are analysed en masse, simplifies the effort by reducing the total number of parallel experiments required. However, this approach generates large amounts of hybridization-based data that must be carefully analysed, assimilated, and disambiguated in a careful but efficient manner.

Results: To facilitate the screening of high-density clone arrays by a multiplex hybridization approach, we have written a program called ComboScreen. This program provides an organizational framework and analytical tools required for the high-throughput hybridization screening of clone arrays with pools of probes. We have used this program extensively for constructing mouse sequence-ready BAC contig maps.

Availability: ComboScreen is freely available at http://genome.nhgri.nih.gov/comboscreen

Contact: cjamison{at}informaxinc.com, egreen{at}nhgri.nih.gov

To whom correspondence should be addressed.


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